Techniques in helical scanning, dynamic imaging and image segmentation for improved quantitative analysis with X-ray micro-CT

This paper reports on recent advances at the micro-computed tomography facility at the Australian National University. Since 2000 this facility has been a significant centre for developments in imaging hardware and associated software for image reconstruction, image analysis and image-based modelling. In 2010 a new instrument was constructed that utilises theoretically-exact image reconstruction based on helical scanning trajectories, allowing higher cone angles and thus better utilisation of the available X-ray flux. We discuss the technical hurdles that needed to be overcome to allow imaging with cone angles in excess of 60°. We also present dynamic tomography algorithms that enable the changes between one moment and the next to be reconstructed from a sparse set of projections, allowing higher speed imaging of time-varying samples. Researchers at the facility have also created a sizeable distributed-memory image analysis toolkit with capabilities ranging from tomographic image reconstruction to 3D shape characterisation. We show results from image registration and present some of the new imaging and experimental techniques that it enables. Finally, we discuss the crucial question of image segmentation and evaluate some recently proposed techniques for automated segmentation

Partially Coherent Lab Based X-ray Micro Computed Tomography

X-ray micro computed tomography (CT) is a useful tool for imaging 3-D internal structures. It has many applications in geophysics, biology and materials science. Currently, micro-CT’s capability are limited due to validity of assumptions used in modelling the machines’ physical properties, such as penumbral blurring due to non-point source, and X-ray refraction. Therefore many CT research in algorithms and models are being carried out to overcome these limitations. This thesis presents methods to improve image resolution and noise, and to enable material property estimation of the micro-CT machine developed and in use at the ANU CTLab. This thesis is divided into five chapters as outlined below. The broad background topics of X-ray modelling and CT reconstruction are explored in Chapter 1, as required by later chapters. It describes each X-ray CT component, including the machines used at the ANU CTLab. The mathematical and statistical tools, and electromagnetic physical models are provided and used to characterise the scalar X-ray wave. This scalar wave equation is used to derive the projection operator through matter and free space, and basic reconstruction and phase retrieval algorithms. It quantifies the four types of X-ray interaction with matter for X-ray energy between 1 and 1000 keV, and presents common assumptions used for the modelling of lab based X-ray micro-CT. Chapter 2 is on X-ray source deblurring. The penumbral source blurring for X-ray micro-CT systems are limiting its resolution. This chapter starts with a geometrical framework to model the penumbral source blurring. I have simulated the effect of source blurring, assuming the geometry of the high-cone angle CT system, used at the ANU CTLab. Also, I have developed the Multislice Richardson-Lucy method that overcomes the computational complexity of the conjugate gradient method, while produces less artefacts compared to the standard Richardson-Lucy method. Its performance is demonstrated for both simulated and real experimental data. X-ray refraction, phase contrast and phase retrieval (PR) are investigated in Chapter 3. For weakly attenuating samples, intensity variation due to phase contrast is a significant fraction of the total signal. If phase contrast is incorrectly modelled, the reconstruction would not correctly account the phase contrast, therefore it would contribute to undesirable artefacts in the reconstruction volume. Here I present a novel Linear Iterative multi-energy PR algorithm. It enables material property estimation for the near field submicron X-ray CT system and reduces the noise and artefacts. This PR algorithm expands the validity range in comparison to the single material and data constrained modelling methods. I have also extended this novel PR algorithm to assume a polychromatic incident spectrum for a non-weakly absorbing object. Chapter 4 outlines the space filling X-ray source trajectory and reconstruction, on which I contributed in a minor capacity. This space filling trajectory reconstruction have improved the detector utilisation and reduced nonuniform resolution over the state-of-the-art 3-D Katsevich’s helical reconstruction, this patented work was done in collaboration with FEI Company. Chapter 5 concludes my PhD research work and provides future directions revealed by the present research

On the investigation of a novel x-ray imaging techniques in radiation oncology

Radiation therapy is indicated for nearly 50% of cancer patients in Australia. Radiation therapy requires accurate delivery of ionising radiation to the neoplastic tissue and pre-treatment in situ x-ray imaging plays an important role in meeting treatment accuracy requirements. Four dimensional cone-beam computed tomography (4D CBCT) is one such pre-treatment imaging technique that can help to visualise tumour target motion due to breathing at the time of radiation treatment delivery. Measuring and characterising the target motion can help to ensure highly accurate therapeutic x-ray beam delivery. In this thesis, a novel pre-treatment x-ray imaging technique, called Respiratory Triggered 4D cone-beam Computed Tomography (RT 4D CBCT), is conceived and investigated. Specifically, the aim of this work is to progress the 4D CBCT imaging technology by investigating the use of a patient’s breathing signal to improve and optimise the use of imaging radiation in 4D CBCT to facilitate the accurate delivery of radiation therapy. These investigations are presented in three main studies: 1. Introduction to the concept of respiratory triggered four dimensional conebeam computed tomography. 2. A simulation study exploring the behaviour of RT 4D CBCT using patientmeasured respiratory data. 3. The experimental realisation of RT 4D CBCT working in a real-time acquisitions setting. The major finding from this work is that RT 4D CBCT can provide target motion information with a 50% reduction in the x-ray imaging dose applied to the patient

Gas hydrate in fine-grained sediments — laboratory studies and coupled processes analyses

Methane hydrates in marine and permafrost sediments are potential energy resources (Boswell, 2009; Collett, 2002). The total amount of carbon trapped in gas hydrate exceeds the sum of all other forms of conventional fossil fuels (Kvenvolden, 1988). However, the dissociation of methane hydrates can accelerate climate change (Archer, 2007; Ruppel and Pohlman, 2008), cause ground subsidence and trigger seafloor landslides (Grozic, 2010; Hornbach et al., 2007; Kvalstad et al., 2005). Hydrate-bearing sands are considered most favorable for future gas production (Boswell and Collett, 2006; Boswell, 2009; Boswell and Collett, 2011). However, over 90% percent of the global hydrate mass is found in fine-grained sediments (Boswell and Collett, 2008). To date, there has been minimal research in hydrate-bearing fine-grained sediments. The central themes of this research are the fundamental understanding of hydrate formation and dissociation in fine-grained sediments, and the associated physical processes. The discussion ranges from the particle-scale to the macro-scale. This includes the shift in the phase boundary associated to curvature effects, the particle-displacive morphology, diffusion induced Leisegang bands and two hydrate formation patterns in gas-filled openings. We develop laboratory techniques that emulate natural gas hydrate formations. The experimental results illustrate the hydrate formation process via different strategies that aim to accelerate the gas supply to the hydrate formation front. In addition, simulations of physical properties of hydrate-bearing fine-grained sediments address the segregated morphology of hydrates in fine-grained sediments and the change in physical properties induced by cryogenic suction. We explore potential methods to produce gas from hydrate-bearing fine-grained sediments. The analyses on gas production centers on the technical viability of depressurization, thermal stimulation and chemical stimulation.Ph.D

Task-Driven Trajectory Design for Endovascular Embolization

Computed Tomography (CT) is one of the most useful and widely applied imaging modalities, employed in both diagnostic and treatment planning purposes in the medical field. Circular and spiral acquisition trajectories are traditionally employed and work well in many cases. The advent of technologies such as robotic C-arms in interventional imaging allow for more complex data acquisitions, which enables potential improvements in image quality, increased field of view, and sampling. This capability has particular potential crucial in interventional cases where images may be compromised by complex anatomy or surgical tools. In this work, we present a paradigm that uses custom non-circular orbits and prior patient information along with segmentation and registration techniques to account for surgical tools and/or implants, to improve image quality. The framework leverages the anatomical model to optimize a parameterized source-detector trajectory for a variety of specific imaging tasks. We propose an overall workflow for orbit customization with investigations of the various workflow stages as well as the overall performance of the framework